Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations. Ubiquitinpathway genes tend to be upregulated in cancermediated by diverse mechanisms. By integratingpan-cancer multiomic data, we identify a group oftumor samples that exhibit worse prognosis. Thesesamples are consistently associated with the upre-gulation of cell-cycle and DNA repair pathways, char-acterized by mutatedTP53,MYC/TERTamplifica-tion, andAPC/PTENdeletion. Our analysishighlights the importance of the ubiquitin pathwayin cancer development and lays a foundation fordeveloping relevant therapeutic strategies

Selected abstracts from the Breastfeeding and Feminism International Conference 2016

Table of contents A1. Infant feeding and poverty: a public health perspective in a global context Lisa H. Amir A2. Mothers’ experiences with galactagogues for lactation: an exploratory cross sectional study Alessandra Bazzano, Shelley Thibeau, Katherine P. Theall A3. The motherhood journey and breastfeeding: from self-efficacy to resilience and social stigma Anna Blair, Karin Cadwell A4. Breastfeeding as an evolutionary adaptive behavior Emily A. Bronson A5. Conflict-of-interest in public health policy: as real as that logo on your website Elizabeth C. Brooks A6. Co-opting sisterhood and motherhood: behind the scenes of Similac’s aggressive social media campaigns Jodine Chase A7. The exclusion of women from the definition of exclusive breastfeeding Ellen Chetwynd, Rebecca Costello, Kathryn Wouk A8. Healthy maternity policies in the workplace: a state health department’s experience with the “Bring Your Infant to Work” program Lindsey Dermid-Gray A9. Implications for a paradigm shift: factors related to breastfeeding among African American women Stephanie Devane-Johnson, Cheryl Woods Giscombe, Miriam Labbok A10. Social experiences of breastfeeding: building bridges between research and policy: an ESRC-funded seminar series in the UK Sally Dowling A11. Manager’s perspectives of lactation breaks Melanie Fraser A12. The challenging second night: a dialogue from two perspectives Jane Grassley, Deborah McCarter-Spaulding, Becky Spencer A13. The role of lactation consultants in two council breastfeeding services in Melbourne, Australia – some preliminary impressions Jennifer Hocking, Pranee Liamputtong A14. Integrating social marketing and community engagement concepts in community breastfeeding programs Sheree H. Keitt, Harumi Reis-Reilly A15. What happens before and after the maternity stay? Creating a community-wide Ten Steps approach Miriam Labbok A16. #RVABREASTFEEDS: cultivating a breastfeeding-friendly community Leslie Lytle A17. Public health vs. free trade: a longitudinal analysis of a global policy to protect breastfeeding Mary Ann Merz A18. Legislative advocacy and grassroots organizing for improved breastfeeding laws in Virginia Kate Noon A19. Breastfeeding and the rights of incarcerated women Krista M Olson A20. Barriers and support for Puerto Rican breastfeeding working mothers Ana M. Parrilla-Rodríguez, José J. Gorrín-Peralta Melissa Pellicier, Zeleida M. Vázquez-Rivera A21. Pumping at work: a daily struggle for Puerto Rican breastfeeding mothers in spite of the law Melissa Pellicier A22. “I saw a wrong and I wanted to stand up for what I thought was right:” a narrative study on becoming a breastfeeding activist Jennifer L. Pemberton A23. Peer breastfeeding support: advocacy and action Catherine McEvilly Pestl A24. Good intentions: a study of breastfeeding intention and postpartum realities among first-time Central Brooklyn mothers Jennifer Pierre, Philip Noyes, Khushbu Srivastava, Sharon Marshall-Taylor A25. Women describing the infant feeding choice: the impact of the WIC breastfeeding classes on infant feeding practices in Ionia, Michigan Jennifer Proto, Sarah Hyland Laurie Brinks A26. Local and state programs and national partnership to reduce disparities through community breastfeeding support Harumi Reis-Reilly, Martelle Esposito, Megan Phillippi A27. Beyond black breastfeeding week: instagram image content analysis for #blackwomendobreastfeed/#bwdbf Cynthia L. Sears, Delores James, Cedric Harville, Kristina Carswell A28. Stakeholder views of breastfeeding education in the K-12 environment: a review of the literature Nicola Singletary, L. Suzanne Goodell, April Fogleman A29. “The Breastfeeding Transition”: a framework for explaining changes in global breastfeeding rates as related to large-scale forces shaping the status of women Paige Hall Smith A30. Breastfeeding, contraception, and ethics, oh my! Advocacy and informed decision-making in the post-partum period Alison M. Stuebe, Amy G. Bryant, Anne Drapkin Lyerly A31. A hard day’s night: juggling nighttime breastfeeding, sleep, and work Cecilia Tomori A32. Empowering change in Indian country through breastfeeding education Amanda L. Watkins, Joan E. Dodgson A33. Servants and “Little Mothers” take charge: work, class, and breastfeeding rates in the early 20th-century U.S. Jacqueline H. Wol

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation

Molecular characterization and clinical relevance of metabolic expression subtypes in human cancers.

Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabolic processes and assessed their clinical relevance. Our metabolic expression subtypes correlated extensively with clinical outcome: subtypes with upregulated carbohydrate, nucleotide, and vitamin/cofactor metabolism most consistently correlated with worse prognosis, whereas subtypes with upregulated lipid metabolism showed the opposite. Metabolic subtypes correlated with diverse somatic drivers but exhibited effects convergent on cancer hallmark pathways and were modulated by highly recurrent master regulators across cancer types. As a proof-of-concept example, we demonstrated that knockdown of SNAI1 or RUNX1—master regulators of carbohydrate metabolic subtypes-modulates metabolic activity and drug sensitivity. Our study provides a system-level view of metabolic heterogeneity within and across cancer types and identifies pathway cross-talk, suggesting related prognostic, therapeutic, and predictive utility

Single nucleotide polymorphism (SNP) - genotyping of Community Acquired Methicillin-Resistant Staphylococcus aureus, including the subtyping of PVL toxin producers using Real-Time PCR

Staphylococcus aureus is a common pathogen that causes a variety of infections including soft tissue infections, impetigo, septicemia toxic shock and scalded skin syndrome. Traditionally, Methicillin-Resistant Staphylococcus aureus (MRSA) was considered a Hospital-Acquired (HA) infection. It is now recognised that the frequency of infections with MRSA is increasing in the community, and that these infections are not originating from hospital environments. A 2007 report by the Centers for Disease Control and Prevention (CDC) stated that Staphylococcus aureus is the most important cause of serious and fatal infections in the USA. Community-Acquired MRSA (CA-MRSA) are genetically diverse and distinct, meaning they are able to be identified and tracked by way of genotyping. Genotyping of MRSA using Single nucleotide polymorphisms (SNPs) is a rapid and robust method for monitoring MRSA, specifically ST93 (Queensland Clone) dissemination in the community. It has been shown that a large proportion of CA-MRSA infections in Queensland and New South Wales are caused by ST93. The rationale for this project was that SNP analysis of MLST genes is a rapid and cost-effective method for genotyping and monitoring MRSA dissemination in the community. In this study, 16 different sequence types (ST) were identified with 41% of isolates identified as ST93 making it the predominate clone. Males and Females were infected equally with an average patient age of 45yrs. Phenotypically, all of the ST93 had an identical antimicrobial resistance pattern. They were resistant to the β-lactams – Penicillin, Flu(di)cloxacillin and Cephalothin but sensitive to all other antibiotics tested. Virulence factors play an important role in allowing S. aureus to cause disease by way of colonising, replication and damage to the host. One virulence factor of particular interest is the toxin Panton-Valentine leukocidin (PVL), which is composed of two separate proteins encoded by two adjacent genes. PVL positive CA-MRSA are shown to cause recurrent, chronic or severe skin and soft tissue infections. As a result, it is important that PVL positive CA-MRSA is genotyped and tracked. Especially now that CA-MRSA infections are more prevalent than HA-MRSA infections and are now deemed endemic in Australia. 98% of all isolates in this study tested positive for the PVL toxin gene. This study showed that PVL is present in many different community based ST, not just ST93, which were all PVL positive. With this toxin becoming entrenched in CA-MRSA, genotyping would provide more accurate data and a way of tracking the dissemination. PVL gene can be sub-typed using an allele-specific Real-Time PCR (RT-PCR) followed by High resolution meltanalysis. This allows the identification of PVL subtypes within the CA-MRSA population and allow the tracking of these clones in the community